X1.C3.3

Overview
NameX1.C3.3
Smed IDSMED30005838
Length (bp)270
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of X1.C3.3 (SMED30005838) t-SNE clustered cells

Violin plots show distribution of expression levels for X1.C3.3 (SMED30005838) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of X1.C3.3 (SMED30005838) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for X1.C3.3 (SMED30005838) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020




SMED30005838

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 25

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000058321.1 SMESG000058307.1 Contig10445uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000058321.1 SMESG000058307.1 Contig10445newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000058321.1 SMESG000058307.1 Contig14928uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000058321.1 SMESG000058307.1 Contig14928newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000058321.1 SMESG000058307.1 Contig46612newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000058321.1 SMESG000058307.1 Contig14927uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000058321.1 SMESG000058307.1 Contig14927newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000025362.1 Contig14926uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000025362.1 Contig14926newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000068042.1 SMESG000058321.1 SMESG000058307.1 SMESG000044801.1 SMESG000002786.1 Contig17705uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005838SMESG000068042.1 SMESG000058321.1 SMESG000058307.1 SMESG000044801.1 SMESG000002786.1 Contig17705newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v6_68_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30005838SMESG000058321.1 SMESG000058307.1 OX_Smed_1.0.14080ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
body wall musculatureSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v4_68_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30005838SMESG000058321.1 SMESG000058307.1 dd_Smed_v6_68_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of X1.C3.3 vs. TrEMBL
Match: V9XRS6 (X1.C3.3 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 144.436 bits (363), Expect = 4.265e-43
Identity = 87/87 (100.00%), Postives = 87/87 (100.00%), Query Frame = 1
Query:    4 MQLIFVLIGLVAIVPLICNGXXXXXXXXXXXXXXXFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKVVSNQCKFNGHACRAS 264
            MQLIFVLIGLVAIVPLICNGNKVEKVEKKVKLLNEFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKVVSNQCKFNGHACRAS
Sbjct:    1 MQLIFVLIGLVAIVPLICNGNKVEKVEKKVKLLNEFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKVVSNQCKFNGHACRAS 87          
BLAST of X1.C3.3 vs. Planmine SMEST
Match: SMESG000058321.1 (SMESG000058321.1)

HSP 1 Score: 142.51 bits (358), Expect = 5.050e-46
Identity = 85/87 (97.70%), Postives = 86/87 (98.85%), Query Frame = 1
Query:    4 MQLIFVLIGLVAIVPLICNGXXXXXXXXXXXXXXXFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKVVSNQCKFNGHACRAS 264
            MQLIFVL GLVAIVPLICNGNKVEKVEKKV+LLNEFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKVVSNQCKFNGHACRAS
Sbjct:    1 MQLIFVLFGLVAIVPLICNGNKVEKVEKKVELLNEFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKVVSNQCKFNGHACRAS 87          
BLAST of X1.C3.3 vs. Planmine SMEST
Match: SMESG000058307.1 (SMESG000058307.1)

HSP 1 Score: 112.079 bits (279), Expect = 4.901e-34
Identity = 71/75 (94.67%), Postives = 74/75 (98.67%), Query Frame = 1
Query:    4 MQLIFVLIGLVAIVPLICNGXXXXXXXXXXXXXXXFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKVVSN 228
            MQLIFVL GLVAIVPLICNGNKVEKVEKKVKLLNEFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKV+++
Sbjct:    1 MQLIFVLFGLVAIVPLICNGNKVEKVEKKVKLLNEFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKVLTS 75          
BLAST of X1.C3.3 vs. Planmine SMEST
Match: SMESG000058307.1 (SMESG000058307.1)

HSP 1 Score: 111.309 bits (277), Expect = 9.204e-34
Identity = 71/74 (95.95%), Postives = 72/74 (97.30%), Query Frame = 1
Query:    4 MQLIFVLIGLVAIVPLICNGXXXXXXXXXXXXXXXFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKVVS 225
            MQLIFVL GLVAIVPLICNGNKVEKVEKKVKLLNEFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYK+ S
Sbjct:    1 MQLIFVLFGLVAIVPLICNGNKVEKVEKKVKLLNEFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKLTS 74          
BLAST of X1.C3.3 vs. Planmine SMEST
Match: SMESG000058307.1 (SMESG000058307.1)

HSP 1 Score: 110.923 bits (276), Expect = 2.826e-33
Identity = 71/72 (98.61%), Postives = 71/72 (98.61%), Query Frame = 1
Query:    4 MQLIFVLIGLVAIVPLICNGXXXXXXXXXXXXXXXFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKV 219
            MQLIFVL GLVAIVPLICNGNKVEKVEKKVKLLNEFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKV
Sbjct:    1 MQLIFVLFGLVAIVPLICNGNKVEKVEKKVKLLNEFEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKV 72          
BLAST of X1.C3.3 vs. Planmine SMEST
Match: SMESG000058307.1 (SMESG000058307.1)

HSP 1 Score: 79.7221 bits (195), Expect = 2.321e-21
Identity = 37/37 (100.00%), Postives = 37/37 (100.00%), Query Frame = 1
Query:  109 FEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKV 219
            FEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKV
Sbjct:    5 FEDLKEEEVKITCPATDKRYCGKSGKPCVTCTTQYKV 41          
The following BLAST results are available for this feature:
BLAST of X1.C3.3 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XRS64.265e-43100.00X1.C3.3 OS=Schmidtea mediterranea OX=79327 PE=2 SV... [more]
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BLAST of X1.C3.3 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.C3.3 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000058321.15.050e-4697.70SMESG000058321.1[more]
SMESG000058307.14.901e-3494.67SMESG000058307.1[more]
SMESG000058307.19.204e-3495.95SMESG000058307.1[more]
SMESG000058307.12.826e-3398.61SMESG000058307.1[more]
SMESG000058307.12.321e-21100.00SMESG000058307.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005838 ID=SMED30005838|Name=X1.C3.3|organism=Schmidtea mediterranea sexual|type=transcript|length=270bp
GACATGCAATTAATATTTGTTTTAATCGGTTTAGTGGCAATCGTTCCGTT
GATTTGCAACGGTAACAAAGTTGAAAAGGTAGAAAAGAAAGTGAAACTTT
TGAATGAGTTCGAAGACTTGAAGGAAGAAGAAGTCAAAATAACCTGTCCA
GCAACCGACAAGAGATATTGTGGTAAATCAGGAAAACCTTGCGTTACTTG
CACTACACAATATAAAGTGGTAAGTAATCAATGCAAATTCAACGGACATG
CGTGCCGCGCTTCATAAACA
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Aliases
The feature 'X1.C3.3' has the following synonyms
Synonym
X1.C3.3
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0000240body wall musculature
PLANA:0000418head
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 23..43
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..21
score: 0.65
NoneNo IPR availableTMHMMTMhelixcoord: 4..21